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Citation for Study 13997

Citation title: "Dinoflagellate phylogeny revisited: Using ribosomal proteins to resolve deep branching dinoflagellate clades ".

Study name: "Dinoflagellate phylogeny revisited: Using ribosomal proteins to resolve deep branching dinoflagellate clades ".

This study is part of submission 13997 (Status: Published).

Citation

Bachvaroff T.R., Gornik S.G., Concepcion G.T., Waller R.F., Mendez G.S., Lippmeier J.C., & Delwiche C. 2013. Dinoflagellate phylogeny revisited: Using ribosomal proteins to resolve deep branching dinoflagellate clades. Molecular Phylogentics and Evolution, .

Authors

• Bachvaroff T.R. (submitter) 301 367 0559
• Gornik S.G.
• Concepcion G.T.
• Waller R.F.
• Mendez G.S.
• Lippmeier J.C.
• Delwiche C.

Abstract

The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these ?protist? taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale RNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean lineages Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 75 ribosomal protein-coding genes were selected for phylogeny. After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts. Overall the tree was well resolved and supported, even when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test. The deepest branches of the dinoflagellate tree can now be resolved with strong support. Despite the strong support for the foundations of the dinoflagellate clade, the relationships within the core dinoflagellate clade remain uncertain. Simple gain or loss scenarios for lifestyle and cell biology features within dinoflagellates and apicomplexans are not entirely consistent with the phylogeny, as well-defined synapomorphic characters are not available.  

Keywords

dinoflagellate, alveolate, heterokont, apicomplexan, ribosomal protein

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S13997
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref21827,
  	 author = {Tsvetan Radoslavov Bachvaroff and Sebastian  G Gornik and Gregory Thomas Concepcion and Ross F Waller and Gregory S Mendez and J Casey Lippmeier and Charles F.  Delwiche},
  	 title = {Dinoflagellate phylogeny revisited:  Using ribosomal proteins to  resolve deep branching dinoflagellate clades },
  	 year = {2013},
  	 keywords = {dinoflagellate, alveolate, heterokont, apicomplexan, ribosomal protein},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Phylogentics and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans.  Together these ?protist? taxa play key roles in primary production and ecology, as well as in illness of humans and other animals.  The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale RNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean lineages Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 75 ribosomal protein-coding genes were selected for phylogeny.  After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts.  Overall the tree was well resolved and supported, even when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test.  The deepest branches of the dinoflagellate tree can now be resolved with strong support. Despite the strong support for the foundations of the dinoflagellate clade, the relationships within the core dinoflagellate clade remain uncertain.  Simple gain or loss scenarios for lifestyle and cell biology features within dinoflagellates and apicomplexans are not entirely consistent with the phylogeny, as well-defined synapomorphic characters are not available.
   
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 21827
  AU  - Bachvaroff,Tsvetan Radoslavov
  AU  - Gornik,Sebastian  G
  AU  - Concepcion,Gregory Thomas
  AU  - Waller,Ross F
  AU  - Mendez,Gregory S
  AU  - Lippmeier,J Casey
  AU  - Delwiche,Charles F. 
  T1  - Dinoflagellate phylogeny revisited:  Using ribosomal proteins to  resolve deep branching dinoflagellate clades 
  PY  - 2013
  KW  - dinoflagellate
  KW  - alveolate
  KW  - heterokont
  KW  - apicomplexan
  KW  - ribosomal protein
  UR  - http://dx.doi.org/
  N2  - The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans.  Together these ?protist? taxa play key roles in primary production and ecology, as well as in illness of humans and other animals.  The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale RNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean lineages Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 75 ribosomal protein-coding genes were selected for phylogeny.  After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts.  Overall the tree was well resolved and supported, even when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test.  The deepest branches of the dinoflagellate tree can now be resolved with strong support. Despite the strong support for the foundations of the dinoflagellate clade, the relationships within the core dinoflagellate clade remain uncertain.  Simple gain or loss scenarios for lifestyle and cell biology features within dinoflagellates and apicomplexans are not entirely consistent with the phylogeny, as well-defined synapomorphic characters are not available.
   
  
  L3  - 
  JF  - Molecular Phylogentics and Evolution
  VL  - 
  IS  - 
  ER  -